TaxSEA-in-python 0.1.5

A small package for converting bacterial names into NCBI IDs

TaxSEA_in_python project

This package is a version of TaxSEA but build in python. Here is the link to the original in R: https://github.com/feargalr/TaxSEA.

Installation

pip install TaxSEA_in_python

Usage

# Import the Python-based implementation of TaxSEA, originally developed as an R tool.
from TaxSEA_in_python.TaxSEA import TaxSEA

# Locate the test data file within the package then run the TaxSEA function on the test data.
from importlib.resources import files 

TaxSEA_test_data = str(files('TaxSEA_in_python.data').joinpath('TaxSEA_test_data.csv'))

TaxSEA_test_results = TaxSEA(TaxSEA_test_data)

# Running TaxSEA with either csv or tsv file
file_path = 'path/to/your/file.csv'

TaxSEA(TaxSEA_test_data, Output_location=file_path)

print(TaxSEA_test_results)

# Access the three DataFrames returned in the TaxSEA_test_results dictionary.
Metabolite_producers = TaxSEA_test_results["Metabolite_producers"]

BugSigdB = TaxSEA_test_results["BugSigdB"]

Health_associations = TaxSEA_test_results["Health_associations"]

"""